Evolution of eukaryotes and organelles is one of the most fundamental topics of biology. Plastids and mitochondria are derived from endosymbiosis between bacteria and ancestral eukaryotes (most likely archeae), and gave significant metabolic advantages to eukaryotes. This study aimed at (1) identification of various primary and secondary (endo)symbiosis in nature and elucidation of shared fundamental mechanisms, (2) elucidation of physiological functions and mechanisms of quality control of such endosymbiosis-derived organelles, (3) establishment of a new paradigm of “endosymbiosis-driven evolution of eukaryotes”, which we named “Matryoshka-type evolution”, and (4) development of synthetic biological methods that allow artificial evolution of cell functions, such as addition of new metabolic functions to organelles and organelle manipulation/transfer.